Rollback of Variant-related changes of r1585, additional PGC code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1586 348d0f76-0448-11de-a6fe-93d51630548a
@VariantEvalWalker - added a command line option to input a file path to a pooled call file for pooled genotype concordance checking. This string is to be passed to the PooledGenotypeConcordance object.
@AllelicVariant - added a method isPooled() to distinguish pooled AllelicVariants from unpooled ones.
@ all the rest - implemented isPooled(); for everything other than PooledEMSNProd it simply returns false, for PooledEMSNProd it returns true.
Added:
@PooledGenotypeConcordance - takes in a filepath to a pool file with the names of hapmap individuals for concordance checking with pooled calls
and does said concordance checking over all pools. Commented out as all the methods are as yet unwritten.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1585 348d0f76-0448-11de-a6fe-93d51630548a
-Remove KGenomesSNPROD
-Remove rodFLT
-Renamed rodGFF to RodGenotypeChipAsGFF
-Fixed a problem in SSGenotypeCall
-Added basic SSGenotype Test class
-Make VCFHeader constructors public
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1536 348d0f76-0448-11de-a6fe-93d51630548a
aaron
depristo
chartl